Dialga G Lv.X is one of the better counters to Vileplume, but my personal favorite is running a second Azelf (Which is useful in Gyarados anyway) and a few Psychic Energies to trap their Spiritombs. If you run Luxray GL Lv.X, it's even better, because you can drag up a Plume and trap it with Lock Up. Dialga is the better counter, but the Azelf takes less deck space, and is useful in matchups other than ???+Vileplume.